Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 26163.32 
• Atom Count: 1708 
• Residue Count: 229 
• Unique protein chains: 1

5NYH

Crystal Structure of Hsp90-alpha N-Domain in complex with Indazole derivative

• DOI: 10.2210/pdb5NYH/pdb

• Classification: CHAPERONE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2017-05-11 Released: 2018-04-18 
• Deposition Author(s): Amaral, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.226 
• R-Value Work: 0.207 

Literature

Ligand Desolvation Steers On-Rate and Impacts Drug Residence Time of Heat Shock Protein 90 (Hsp90) Inhibitors.

Schuetz, D.A., Richter, L., Amaral, M., Grandits, M., Gradler, U., Musil, D., Buchstaller, H.P., Eggenweiler, H.M., Frech, M., Ecker, G.F.

(2018) J. Med. Chem. 61: 4397-4411

• PubMed: 29701469 
• DOI: 10.1021/acs.jmedchem.8b00080
• Primary Citation of Related Structures:  
  5ODX, 5OCI, 5OD7, 5LO1, 5LO0, 5LNZ, 5LNY


• PubMed Abstract: 
  

Residence time and more recently the association rate constant k _on are increasingly acknowledged as important parameters for in vivo efficacy and safety of drugs. However, their broader consideration in drug development is limited by a lack of knowledge of how to optimize these parameters. In this study on a set of 176 heat shock protein 90 inhibitors, structure-kinetic relationships, X-ray crystallography, and molecular dynamics simulations were combined to retrieve a concrete scheme of how to rationally slow down on-rates. We discovered that an increased ligand desolvation barrier by introducing polar substituents resulted in a significant k _on decrease. The slowdown was accomplished by introducing polar moieties to those parts of the ligand that point toward a hydrophobic cavity. We validated this scheme by increasing polarity of three Hsp90 inhibitors and observed a 9-, 13-, and 45-fold slowdown of on-rates and a 9-fold prolongation in residence time. This prolongation was driven by transition state destabilization rather than ground state stabilization.

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Organizational Affiliation: 

Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Braunschweig, Germany.,Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China.,the Norwegian College of Fisheries Science, Arctic University of Norway, N-9037 Tromsø, Norway, and.,Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 10691, Stockholm, Sweden.,Department of Theoretical Biophysics, Max Planck Institute of Biophysics, DE-60438, Frankfurt, Germany.,Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, China.,Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, Haidian District, Beijing, China.,Instituto de Estructura de la Materia, Consejo Superior de Investigaciones Científicas IEM-CSIC, Serrano 121, E-28006 Madrid, Spain.,Laboratório de Espectrometria de Massa, Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil. Electronic address: [e-mail].,Department of Molecular and Systems Biology and Norris Cotton Cancer Center , Geisel School of Medicine at Dartmouth , 1 Medical Centre Drive HB7936 , Lebanon , New Hampshire 03756 , United States.,Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, PO Box 5400, FI-90014 Oulu, Finland.,Center of Pharmaceutical Engeneering (PVZ), Technische Universität Braunschweig, Braunschweig, Germany.,Department of Biology, Washington University in St. Louis, One Brookings Drive, Campus Box 1137, St. Louis, MO, 63130, USA.,School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea. [e-mail].,Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou 450001, China.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.,Department of Neurology, Amsterdam Neuroscience, Academic Medical Center, Meidreefberg 9, 1105, AZ, Amsterdam, the Netherlands.,Biomarker Discovery, Novartis Institute for BioMedical Research, Basel, Switzerland.,Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.,RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.,College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001, China.,Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India. Electronic address: [e-mail].,Nosopharm, 110 Allée Charles Babbage, Espace Innovation 2, 30000 Nîmes, France. Electronic address: [e-mail].,ManRos Therapeutics, Hôtel de Recherche, Centre de Perharidy, Roscoff, France.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.,EMD Serono Research & Development Institute, Inc., 45A Middlesex Turnpike, Billerica 01821, MA, USA. Electronic address: [e-mail].,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA; Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan. [e-mail] [e-mail].,Janssen Neuroscience Discovery, Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, 2340, Beerse, Belgium.,ConverGene LLC., 3093 Beverly Lane, Unit C, Cambridge, MD 21613, United States.,Department of Pharmaceutical Science, General and Organic Chemistry Section, University of Milano, 20133 Italy.,University Medical Center Göttingen, Institute of Clinical Chemistry, Bioanalytics Group, Robert-Koch-Straße 40, 37075 Göttingen, Germany.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada. [e-mail].,Tetramer Core, BRI at Virginia Mason, Seattle, WA, USA.,Translational Research Program, BRI at Virginia Mason, Seattle, WA, USA.,School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea.,Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea. [e-mail].,Department of Biology and Chemistry Laboratory of Biomolecular Research, Paul Scherrer Institut (PSI), 5232 Villigen, Switzerland.,Unit of Anti-Viral Immunity and Genetic Therapy, Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China.,Department of Chemistry , University of Florence , Via della Lastruccia 3 , 50019 Sesto Fiorentino, Florence , Italy.,Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China. [e-mail].,Chemical and Physical Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain.,National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States.,Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Structural Biology Group, European Synchrotron Radiation Facility, CS 40220, F-38043, Grenoble, France. [e-mail].,Center for Integrated Protein Science at the Department Chemistry, Chair of Biochemistry, Technical University of Munich, Lichtenbergstr. 4, 85748, Garching, Germany. [e-mail].,Pfizer Structural Biology and Biophysics, Groton, Eastern Point Road, Groton, CT 06340, USA.,Laboratoire de Microbiologie, Université libre de Bruxelles (ULB), 6041 Gosselies, Belgium.,Ben May Department for Cancer Research, University of Chicago, Chicago, IL, 60637, USA. [e-mail].,Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany. [e-mail].,RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.,Faculty of Science, University of Zurich, Zurich, 8057, Switzerland.,Present address: Janssen R&D US, 3210 Merryfield Row, San Diego, CA, 92121, USA.,Department of Biological Sciences, University of Wisconsin, Milwaukee, WI 53201, USA.,Janssen Vaccines and Prevention, Janssen Pharmaceutical Companies of Johnson and Johnson, Archimedesweg 6, Leiden, CN, 2333, the Netherlands.,Department of Dermatology and Allergy Biederstein, Technical University of Munich, Biedersteiner Str. 29, 80802, Munich, Germany.,Astex Pharmaceuticals , 436 Cambridge Science Park , Cambridge , CB4 0QA , UK . Email: [e-mail] ; Email: [e-mail].,Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Republic of Korea [e-mail].,Focus Group "Clinical Cell Processing and Purification", Institute for Advanced Study, Technical University of Munich, 81675, Munich, Germany. [e-mail].,Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Hefei National Laboratory for Physical Sciences at Microscale,CAS Key Laboratory of Brain Function and Disease, Neurodegenerative Disorder Research Center, School of Life Sciences, University of Science and Technology of China, Hefei, China.,Chair of Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Weihenstephan, Germany.,Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Trogerstr. 30, 81675, Munich, Germany. [e-mail].,State Key Laboratory for Infectious Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China, and.,Department of Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel.,RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan. [e-mail].,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA. [e-mail].,German Center for Infection Research (DZIF), Trogerstr. 30, 81675, Munich, Germany. [e-mail].,Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea.,Howard Hughes Medical Institute, Seattle, WA, USA.,Institute of Pathology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Université de Lorraine, INRA, IAM, Nancy, France. [e-mail].,Department of Chemistry, University of Duisburg-Essen, Universitätsstr. 7, 45117, Essen, Germany.,Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.,Department of Oncology-Pathology , Karolinska Institute , CCK R8:01 , Karolinska Hospital , 171 76 Stockholm , Sweden.,Present address: Department of Molecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, 69120, Heidelberg, Germany.,University Clinic of Visceral Surgery and Medicine, Departement Klinische Forschung, University of Bern, Murtenstr. 35, CH-3010, Bern, Switzerland.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, H3C 3J7, Canada. [e-mail].,High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Center, Mumbai 400 085, India.,International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.,Departments of Chemistry, Immunology, Chemistry Modeling and Informatics, In Vitro Pharmacology, Target Protein Design and Structural Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.,Translational Medicine, Novartis Institute for BioMedical Research, Basel, Switzerland.,Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA.,Graduate School of Innovative Life Science , University of Toyama , 2630 Sugitani , Toyama 930-0194 , Japan.,Institute for Interdisciplinary Science, Okayama University, Okayama, Japan.,Nova Southeastern University Cell Therapy Institute, Dr. Kiran C. Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL 33301.,Department of Chemistry, Syracuse University, Syracuse, NY, 13244, USA.,Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, China. Electronic address: [e-mail].,Arietis Pharma, Boston, Massachusetts, USA [e-mail].,Department of Biochemistry and Molecular Biology and the Center for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada. [e-mail].,the Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316 Oslo, Norway.,Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, MA 02142, USA.,Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, 2333, CN, Leiden, the Netherlands. [e-mail].,Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH), CH-8093, Zürich, Switzerland.,Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.,Department of Chemistry, University of Eastern Finland, PO Box 111, 80101 Joensuu, Finland.,Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, 3210 Merryfield Row, San Diego, CA, 92121, USA.,Musculoskeletal Diseases, Novartis Institute for BioMedical Research, Basel, Switzerland.,European Synchrotron Radiation Facility, Structural Biology Group, 71 Avenue des Martyrs, F-38000, Grenoble, France.,Computational Biochemistry, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany.,RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan. [e-mail].,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6059, USA.,KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea.,Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Université de Lorraine, CNRS, CRM2, Nancy, France. [e-mail].,Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Trogerstr. 30, 81675, Munich, Germany.,Department of Cell Biochemistry, University of Groningen, Groningen 9747 AG, Netherlands.,DISFARM, Dipartimento di Scienze Farmaceutiche, Sezione Chimica Generale e Organica, Università degli Studi, Milano, Italy.,Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada. [e-mail].,Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Institute of Biochemistry, ETH Zurich, 8093, Zurich, Switzerland.,EMD Serono Research & Development Institute, Inc., 45A Middlesex Turnpike, Billerica 01821, MA, USA.,From The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China, [e-mail].,Department of Medical Biochemistry and Microbiology, Uppsala University, 75237 Uppsala, Sweden.,Biochemistry, Cellular, and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA.,Institute for Pharmaceutical Chemistry, Structural Genomics Consortium and Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.,State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.,LOEWE Center for Synthetic Microbiology (Synmikro), Philipps University Marburg, Marburg, Germany.,Department of Computer Science, Tsinghua University, Beijing 100084, China.,Department of Life Sciences and Chemistry, Jacobs University Bremen, 28759 Bremen, Germany.,Pfizer Neuroscience and Pain Research Unit, Granta Park, Great Abington, Cambridge CB21 6GS, UK.,Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India.,Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo, 678-1297, Japan.,Abteilung Physikalische Biochemie, Max-Planck-Institut für molekulare Physiologie, Dortmund, Germany.,Nosopharm, 110 Allée Charles Babbage, Espace Innovation 2, 30000 Nîmes, France.,Institute for Advanced Study, Hong Kong University of Science and Technology, Hong Kong, China.,Instituto de Química, Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil; Departamento de Áreas Acadêmicas, Instituto Federal de Educação, Ciência e Tecnologia e Goiás (IFG), Luziânia, Goiás, Brazil.,Rheumatology Unit, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden. Electronic address: [e-mail].,Global Drug Development, Novartis, Basel, Switzerland.,Medicinal Chemistry , Merck KGaA , 64293 Darmstadt , Germany.,Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH), CH-8093, Zürich, Switzerland. [e-mail].,State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China.,Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg.,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, China.,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, China. Electronic address: [e-mail].,Department of Biochemistry and Molecular Biology and the Center for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada.,From the Department of Cell and Molecular Biology, Uppsala University, Box 596, S-751 24 Uppsala, Sweden.,Instituto de Biologia Experimental e Tecnológica , Oeiras , Portugal.,Max Planck Institute for Evolutionary Anthropology, D-04103, Leipzig, Germany.,Brain Science Institute, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea; Department of Neuroscience, Korea University of Science and Technology, Daejeon, Republic of Korea; Department of Neuroscience, College of Veterinary Medicine, Research Institute for Veterinary Science, and BK21 PLUS Program for Creative Veterinary Science Research, Seoul National University, Seoul, 08826, Republic of Korea.,German Center for Infection Research (DZIF), Trogerstr. 30, 81675, Munich, Germany.,Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Republic of Korea.,Laboratory of Chemical Biology and Institute of, Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands.,Pfizer Structural Biology and Biophysics, Groton, Eastern Point Road, Groton, CT 06340, USA. Electronic address: [e-mail].,Preclinical Safety, Novartis Institute for BioMedical Research, Basel, Switzerland.,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Magnetic Resonance Center CERM , University of Florence , Via Luigi Sacconi 6 , 50019 Sesto Fiorentino, Florence , Italy.,Molecular and Cellular Pharmacology, Discovery Sciences, Janssen Pharmaceutical Companies of Johnson & Johnson, Turnhoutseweg 30, 2340, Beerse, Belgium.,Aix-Marseille Université, IRBA, TMCD2 UMR-MD1, Faculté de Médecine, Marseille, France.,Neuroscience, Novartis Institute for BioMedical Research, Basel, Switzerland.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.,Science for Life Laboratory Department of Theoretical Physics, KTH Royal Institute of Technology, SE-100 44, Stockholm, Sweden.,Laboratoire de Physiologie Cellulaire & Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRA, BIG, Grenoble, USA. [e-mail].,University Chemical Laboratory, University of Cambridge, Cambridge CB2 1EW, U.K.,Rheumatology Unit, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden; Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Sweden; Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden.,European Synchrotron Radiation Facility, Structural Biology Group, 71 Avenue des Martyrs, F-38000, Grenoble, France. [e-mail].,Neuroscience, Novartis Institute for BioMedical Research, Basel, Switzerland [e-mail] [e-mail].,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China, and.,Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 & Université Paris Diderot, 25 rue du Dr. Roux, 75724 Paris CEDEX 15, France. Electronic address: [e-mail].,National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States. Electronic address: [e-mail].,Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, SE-17176 Stockholm, Sweden.,Chemical Biology and Therapeutics, Novartis Institute for BioMedical Research, Basel, Switzerland.,Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 10691, Stockholm, Sweden. [e-mail].,Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany.,Institute of Medical Microbiology, University of Zurich, 8006, Zurich, Switzerland. [e-mail].,Center for Biomolecular Sciences, University of Illinois, Chicago, IL 60607, USA.,Discovery Technologies , Merck KGaA , Frankfurter Straße 250 , 64293 Darmstadt , Germany.,Institut Pasteur, Plate-forme de Cristallographie, CNRS UMR 3528, 25 rue du Dr. Roux, 75724 Paris CEDEX 15, France.,Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, UK.,National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States. Electronic address: [e-mail].,Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.,Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China.,German Center for Diabetes Research (DZD), Ingostädter Landstr. 1, 85764, Neuherberg, Germany.,Institut de Recherches Microbiologiques Jean-Marie Wiame - Labiris, 1070 Brussels, Belgium.,Gorlaeus Laboratories , Leiden Institute of Chemistry and Netherlands Proteomics Centre , Einsteinweg 55 , 2333 CC Leiden , Netherlands.,Ruhr University Bochum, Faculty of Biology and Biotechnology, Department of Biophysics, Protein Crystallography, Universitätsstr. 150, 44780 Bochum, Germany.,Área de Farmacología, Departamento de Ciencias Biomédicas, Universidad de Alcalá, Unidad Asociada al IQM (CSIC), Alcalá de Henares, E-28871 Madrid, Spain.,Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.,F. Hoffmann-La Roche AG, Konzern-Hauptsitz, Grenzacherstrasse 124, CH-4070 Basel, Switzerland.,Institute of Molecular Biology & Biophysics, ETH Zurich, 8093, Zurich, Switzerland. [e-mail].,Department of Pathology, Amsterdam Neuroscience, VU University Medical Center, De Boelelaan 1117, 1081, HV, Amsterdam, the Netherlands.,Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.,Institute for Computational Molecular Science College of Science and Technology, Temple University, 1925 N 12th St, Philadelphia, PA 19122.,Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea. Electronic address: [e-mail].,College of Life Sciences, Peking University, Beijing 100871, China.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, H3C 3J7, Canada.,Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, PO Box 5400, FI-90014 Oulu, Finland [e-mail].,School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.,German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,VIB-VUB Center For Structural Biology, 1050 Brussels, Belgium.,Division of Immunology, Department of Biology, University of Konstanz, Universitaetsstr. 10, 78457, Konstanz, Germany.,DGIMI, INRA, Université de Montpellier, Montpellier, France.,Department of Chemistry, University of Washington, Seattle, Washington.,Department of Biochemistry and the Emory Comprehensive Glycomics Core, Emory University School of Medicine, Atlanta, GA, 30322, USA.,Max Planck Institute for Terrestrial Microbiology, Marburg, Germany. [e-mail].,Department of Dermatology and Allergy Center, Odense Research Center for Anaphylaxis, University of Southern Denmark, DK-5000, Odense C, Denmark.,KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea. [e-mail].,Institute of Biochemistry, University of Cologne, 50674 Koeln, Germany.,Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea.,From The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Olema Pharmaceuticals, San Francisco, CA, 94107, USA. [e-mail].,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, China; Departments of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.,Institute of Human Genetics, Technical University of Munich, 81675, Munich, Germany.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6059, USA. [e-mail].,Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany.,Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie , Technische Universität München , 85748 Garching , Germany.,Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui, China.,Present address: Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.,Department of Pharmacology, Baylor College of Medicine, Houston, TX, 77030, USA.,Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry , University of California , Irvine , California 92697-3900 , United States.,Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China, and [e-mail].,Harvard Medical School, 300 Longwood Ave, Boston, MA 02115.,Department of Chemistry, University of Pennsylvania, 231 S 34th St, Philadelphia, PA 19104.,Departamento de Química, Universidade Federal de São Carlos (UFSCar), São Carlos, São Paulo, Brazil.,Instituto de Química, Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil; Instituto de Biociências, Universidade Federal do Estado do Rio de Janeiro (UNIRIO), Rio de Janeiro, Rio de Janeiro, Brazil.,Institute of Molecular Biology & Biophysics, ETH Zurich, 8093, Zurich, Switzerland.,Division of Structural Biology, Department of Pharmaceutical Sciences, School of Pharmacy, Iwate Medical University, Yahaba, Japan.,Department of Plant Science, Rothamsted Research, Harpenden, Herts AL5 2JQ, United Kingdom.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, 02115, USA.,Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, 2333, CN, Leiden, the Netherlands.,Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.,Olema Pharmaceuticals, San Francisco, CA, 94107, USA.,Key Laboratory for Insect-Pollinator Biology of the Ministry of Agriculture, Institute of Apiculture, Chinese Academy of Agricultural Sciences, Beijing, China.,Pfizer Worldwide Medicinal Chemistry, Neuroscience and Pain Research Unit, Granta Park, Great Abington, Cambridge CB21 6GS, UK.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.,Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA; Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, IL 60607, USA. Electronic address: [e-mail].,Ruhr University Bochum, Fakultät für Medizin, Institute for Biochemistry and Pathobiochemistry, Microbial Biochemistry, Universitätsstr. 150, 44780 Bochum, Germany.,Structural Biology Group, European Synchrotron Radiation Facility, CS 40220, F-38043, Grenoble, France.,Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address: [e-mail].,Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, SE-17176 Stockholm, Sweden; [e-mail].,Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Kyungbuk, 37673, Republic of Korea.,Takeda California, Inc. , 10410 Science Center Drive , San Diego , California 92121 , United States.,Department of Pediatrics, Graduate School of Medicine, Gifu University, Yanagido 1-1, Gifu 501-1194, Japan.,Global Discovery Chemistry, Novartis Institute for BioMedical Research, Basel, Switzerland.,Ben May Department for Cancer Research, University of Chicago, Chicago, IL, 60637, USA.,School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.,Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA. [e-mail].,Center for Integrated Protein Science at the Department Chemistry, Chair of Biochemistry, Technical University of Munich, Lichtenbergstr. 4, 85748, Garching, Germany.,Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, 44195, USA. [e-mail].,Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland.,Institute of Human Genetics, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Department of Neuroscience, College of Veterinary Medicine, Research Institute for Veterinary Science, and BK21 PLUS Program for Creative Veterinary Science Research, Seoul National University, Seoul, 08826, Republic of Korea. Electronic address: [e-mail].,Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, 44195, USA.,Rheumatology Unit, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan. [e-mail] [e-mail].,Department of Chemistry, Université de Montréal, Montréal, QC, H3C 3J7, Canada.,Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada.,Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, AlbaNova University Center, Royal Institute of Technology, SE-10691 Stockholm, Sweden.,Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, Center for Developmental Therapeutics , Northwestern University , 2145 Sheridan Road , Evanston , Illinois 60208-3113 , United States.,Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Sweden; Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden.,Université de Lorraine, INRA, IAM, Nancy, France.,Department of Microbiology, School of Dentistry, Aichi Gakuin University, Nagoya, Japan.,Faculty of Chemistry, Philipps-University-Marburg, Marburg, Germany.,Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China. [e-mail].,Institute of Medical Microbiology, University of Zurich, 8006, Zurich, Switzerland.,Institut Charles Gerhardt Montpellier, UMR 5253 CNRS-UM-ENSCM, Montpellier, France.,Max-Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.,Proteros Biostructures GmbH, Bunsenstraße 7a, 82152, Planegg, Germany.,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, China. Electronic address: [e-mail].,Pfizer Worldwide Research & Development , 610 Main Street, Cambridge, Massachusetts 02139, United States.,Pfizer Neuroscience and Pain Research Unit, Granta Park, Great Abington, Cambridge CB21 6GS, UK. Electronic address: [e-mail].,Bioanalytics Research Group, Department of Clinical Chemistry, University Medical Centre, Göttingen, Germany.,Institute of Molecular Systems Biology, ETH Zurich, 8093, Zurich, Switzerland.,LOEWE Center for Synthetic Microbiology (Synmikro), Philipps University Marburg, Marburg, Germany. [e-mail].,Center for Structural Biology, VIB, B-1050, Brussels, Belgium.,Department of Biochemistry, University of Zurich, 8057, Zurich, Switzerland.,Theodor Boveri Institute of Biosciences (Biocenter), University of Würzburg, Am Hubland, D-97074 Würzburg, Germany.,Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, 793022, India.,Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China [e-mail] [e-mail].,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.,Chemical Biology, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany.,Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.,Institut de Biologie Moleculaire et Cellulaire, Centre National de la Recherche Scientifique, Strasbourg, France.,Center for Biomolecular Sciences, University of Illinois, Chicago, IL 60607, USA. Electronic address: [e-mail].,Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology, Seoul, Republic of Korea.,From the Department of Cell and Molecular Biology, Uppsala University, Box 596, S-751 24 Uppsala, Sweden, [e-mail].,Institut Pasteur de Montevideo, Laboratory of Molecular and Structural Microbiology, Mataojo 2002, Montevideo 11400, Uruguay; Institut Pasteur, Departement de Microbiologie, 25-28 rue du Dr. Roux, 75724 Paris CEDEX 15, France.,Institute of Biophysics, Goethe University, DE-60438, Frankfurt, Germany.,Department of Microbiology, University of Washington, Seattle, WA, USA.,Global Drug Development, Novartis, Basel, Switzerland [e-mail] [e-mail].,Neuroscience Drug Discovery Unit, Research , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome, Fujisawa , Kanagawa 251-8555 , Japan.,Université de Lorraine, LERMAB, Nancy, France.,Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.,Institute for Molecular Animal Breeding and Biotechnology, Gene Center of the Ludwig-Maximilians-Universität München, Feodor-Lynen Str. 25, 81377, Munich, Germany.,Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 & Université Paris Diderot, 25 rue du Dr. Roux, 75724 Paris CEDEX 15, France.,Laboratoire de Physiologie Cellulaire & Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRA, BIG, Grenoble, USA.,Department of Pharmaceutical Chemistry , University of Vienna , UZA 2, Althanstrasse 14 , 1090 Vienna , Austria.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA. [e-mail].,Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore 453 552, India.,Structural Genomics Consortium, Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom.,Department of Chemistry and Biochemistry, University of Berne, CH-3012, Berne, Switzerland.,The Francis Crick Institute, London, NW1 1AT, United Kingdom.,Arietis Pharma, Boston, Massachusetts, USA.,Department of Hematology and Oncology , Kantonsspital St. Gallen , 9007 St. Gallen , Switzerland.,Department of Biochemical Sciences A.Rossi-Fanelli, University of Rome La Sapienza, Rome, Italy.,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA.,PK Sciences, Novartis Institute for BioMedical Research, Basel, Switzerland.,Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany.,Department of Medical Sciences, Rheumatology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Université de Lorraine, CNRS, CRM2, Nancy, France.,Bacteria, Parasites & Fungi, Statens Serum Institut, 2300 Copenhagen, Denmark.,Faculty of Pharmaceutical Sciences , University of Toyama , 2630 Sugitani , Toyama 930-0914 , Japan.,Present address: Department of Physics, University of Warwick, Coventry, CV4 7AL, UK.,Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 & Université Paris Diderot, 25 rue du Dr. Roux, 75724 Paris CEDEX 15, France. Electronic address: [e-mail].,Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.,Laboratório de Espectrometria de Massa, Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil.,Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo, 678-1297, Japan. [e-mail].,School of Biological Science and Technology, University of Jinan, Jinan, China.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Heat shock protein HSP 90-alpha	A	229	Homo sapiens	Mutation(s): 0  Gene Names: HSP90AA1 (HSP90A, HSPC1, HSPCA)
Find proteins for P07900 (Homo sapiens) Go to Gene View: HSP90AA1 Go to UniProtKB:  P07900

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
9EK	A	~{N}-methyl-~{N}-(4-morpholin-4-ylphenyl)-6-oxidanyl-3-pyrrolidin-1-ylcarbonyl-2~{H}-indazole-5-carboxamide C24 H27 N5 O4 PAGPOZMFSDBEOC-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
9EK	Kd: 18.7 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.226 
• R-Value Work: 0.207 
• Space Group: I 2 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 69.979	α = 90.00
b = 88.540	β = 90.00
c = 97.091	γ = 90.00

Software Package:

Software Name	Purpose
BUSTER	refinement
PHASER	phasing
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-05-11 
• Released Date: 2018-04-18 
• Deposition Author(s): Amaral, M.

Revision History 

• Version 1.0: 2018-04-18
  Type: Initial release
• Version 1.1: 2018-05-23
  Type: Data collection, Database references
• Version 1.2: 2018-06-06
  Type: Data collection, Database references